Environmental Molecular Microbiology
"highly recommended ... invaluable" (International Microbiology)
Caister Academic Press
Wen-Tso Liu and Janet K. Jansson
University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA (respectively)
viii + 232
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Molecular biology has revolutionized the study of microorganisms in the environment and improved our understanding of the composition, phylogeny, and physiology of microbial communities. The current molecular toolbox encompasses a range of DNA-based technologies and new methods for the study of RNA and proteins extracted from environmental samples. Currently there is a major emphasis on the application of omics approaches to determine the identities and functions of microbes inhabiting different environments.
This book highlights the current state-of-the-art of environmental molecular microbiology. International experts have contributed chapters that describe the various technologies and their applications in environmental microbiology. The first half of the book focuses on the microbial diversity and phylogeny of microorganisms in the environment and describes the molecular toolbox currently available for the study of the composition and diversity of microbial communities and their functions. Topics include the use of the 16S rRNA gene as a phylogenetic marker, metagenomics, metaproteomics, microarrays, and molecular fingerprinting. The second half focuses on the application of these approaches in various environments including soil, marine water, plants, humans and wastewater treatment. The last chapter of the book discusses the genetics and environmental implications of microbial biofilms.
An essential book for advanced students, research scientists, environmental agencies and industries involved in any aspect of environmental microbiology.
"highly recommended to students and researchers interested in microbial diversity and ecology. The knowledge and methodologies described in the book offer invaluable research tools with which to meet this challenge." from International Microbiology (2009) 12: 254-255.
"a contribution to the advances of molecular techniques in environmental microbiology. More than 30 authors, representing highly recognized institutes such as the Lawrence Berkeley National Laboratory, the Center for Microbial Ecology of the Michigan State University, to name just a few, have contributed to this book ... summarizes the current stat-of-the-art molecular techniques ... will be a useful addition to the libraries of students and professionals" from SciTech Book News
"(recommended) for the newcomer in metagenomics and also for those interested in molecular biology in an ecological context" from Biospektrum (March 2010) p. 366
Table of contents
1. Microbial Diversity and Phylogeny: Extending from rRNAs to Genomes
James R. Cole, Kostas Konstantinidis, Ryan J. Farris and James M. Tiedje
The small subunit ribosomal RNA gene (SSU rRNA) has been the cornerstone of microbial ecology studies over the last 15 years, and has provided much of what we know about Bacterial and Archaeal diversity and community structure, and has greatly aided microbial taxonomy. This chapter provides information on the development of this gene as a molecular marker and tools for its analysis, but also addresses challenges for the future including advancing the species definition, linking 16S rRNA information to taxonomy, the need for finer-grained resolution of community members and how genomics is aiding our understanding of the relationships among closely related organisms, and ultimately of natural populations. When the available 16S rRNA genes from species type strains were examined, the most distant sequences in the median genus and family were about 4.4% and 14% different, respectively. The largest dissimilarity between a sequence and its closest relative in the same taxa (similar to single-linkage clustering distance) was 3.5% and 10% for the median genus and family. The ratio of the two values, a measure of the 'shape' of the taxa averaged less than 1.5 for all ranks, indicating that most taxa are not elongated, but are fairly spherical. When the near-full-length 16S rRNA gene sequences in the public databases in 2006 were clustered into groups at proxy distances for species, genus, family and order, the number of clusters with time increased exponentially for all ranks documenting the enormous diversity of the microbial world and that much remains to be discovered.
2. Genomics and Metagenomics: History and Progress
Karen E. Nelson, Peter A. Bryan and Bryan A. White
The extensive suite of molecular-based approaches developed over the past decade has enabled the field of metagenomics, the study of uncultured microorganisms. Paramont to metagenomic analysis is use of high-throughput DNA sequencing technologies, which with the advent of low cost next-generation methods is transforming metagenomics. The application of metagenomics, to both global environments and microbes associated with a living host, has facilitated study of the functional ecology of environmental microorganisms. Novel functional genes and environmental functional signatures can be retrieved using metagenomics, and these can form the basis of hypothesis driven analyses of uncultured microorganisms. A with any technology, the daunting task is to understand and apply the growing number of metagenomic sequences in the context of microbial ecology and evolution.
3. Metaproteomics: Techniques and Applications
Brian D. Dill, Jacque C. Young, Patricia A. Carey and Nathan C. VerBerkmoes
Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and "omics" technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying functional information concerning microbial activity. Advances in mass spectrometry instrumentation and methodologies, along with bioinformatics approaches, have brought this analytic chemistry technique to relevance in the biological realm due to its powerful applications in proteomics. Mass spectrometry-enabled proteomics, including "bottom-up" and "top-down" approaches, is capable of supplying a wealth of biologically-relevant information, from simple protein cataloging of the proteome of a microbial community to identifying post-translational modifications of individual proteins.
4. Nucleic-Acid-based Characterization of Community Structure and Function
James Prosser, Janet K. Jansson and Wen-Tso Liu
Nucleic acid-based techniques were first used to characterise natural microbial communities in the early 1990s and are now used routinely. The ability to characterise communities without the requirement for cultivation has led to enormous advances in our ability to describe microbial communities and to determine the factors that influence their structure. New generations of molecular techniques provide even greater descriptive power and can be used to assess the physiological potential and ecosystem function of communities. They also enable microbial ecologists to address fundamental questions in population and community ecology, including investigation of the links between diversity and function. This chapter describes methods currently used to analyse nucleic acids extracted from environmental samples, and shows how they can be used to characterise communities. It also looks ahead to exciting new technologies that are likely to increase greatly our ability to explore and understand the complex functions and interactions of microbial communities in natural environments.
5. The Use of Microarrays in Microbial Ecology
Gary L. Andersen, Zhili He, Todd Z. DeSantis, Eoin L. Brodie and Jizhong Zhou
Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning. Examples of the application of both arrays in different environmental samples will be described in the two subsequent sections.
6. The Soil Environment
Kornelia Smalla and Jan Dirk van Elsas
Until fairly recently, the living soil has been considered as a functional black box that is intrinsically too difficult to be unravelled into its core components. However, this concept has changed with the advent of the modern methodologies. Here, we examine how our understanding of the intricacies of microbial life in soil has been impacted by the advanced, mainly molecularly-based, approaches that have been unleashed on the soil habitat in recent years. Truly, although the soil 'microbial black box' is still far from being completely opened, the application of molecular and other advanced methods (allowing the so-called cultivation-independent analyses) has provided exciting new insights into microbial (in particular bacterial) life in soil.
7. Plant-associated Microbial Communities
George A. Kowalchuk, Etienne Yergeau, Johan H.J. Leveau, Angela Sessitsch and Mark Bailey
Plants, both above- and belowground, offer diverse habitats for microbial colonization and growth. Plant-microbe interactions lie at the heart of plant performance and ecology. Plants provide various growth substrates and physical habitats for microbes on both sides of the air-soil interface, and numerous plant-associated niches have been exploited by specific microbial species, either by specializing on the distinct environmental conditions available, or entering into commensal, mutualistic, or parasitic interactions with plants. This chapter seeks to examine the state of the art with respect to our ability to characterize the structure, function and interactions of plant-associated microbial communities, with a particular focus on the role of molecular biological methods and environmental genomics strategies in promoting this field. We will pay particular attention to bacterial and fungal colonization of above and belowground plant surfaces (phyllosphere and rhizosphere, respectively), as well as in planta (endosphere) interactions of endophytic, parasitic and symbiotic microorganisms. Of particular importance to advancing this research field are emerging methodologies, including novel '-omics' approaches, that seek to link microbial identity to in situ functioning, and holistic approaches that capture the complexities involved in multiple plant-microbe interactions.
8. Marine Environments
Alexander H. Treusch, Ulrich Stingl and Stephen J. Giovannoni
Ocean microbial communities play important roles in global geochemical cycles. From the earliest cultivation experiments to today's metagenomic analyses, most of the major discoveries in this field were driven by applications of novel methods. Molecular ecology had a major impact by revealing the true scope of microbial diversity and providing genetic markers that could be used to track important species, even in cases where cultures were unavailable. In some cases, metagenomics provided insight into the biochemical adaptations of these organisms. A renaissance in culturing technique led to isolates of many abundant ocean microbes that could then be studied in a laboratory setting. Today a consortium of approaches that span scales from molecules to ocean basins are being applied to ocean micobial ecosystems, with the result that marine microbiology is becoming a highly integrated science.
9. Human Environment
Johan Dicksved, Liping Zhao and Janet K. Jansson
Applications of recent advances in molecular methods have illuminated the previously hidden diversity of the microbial world that not only inhabits our bodies, but that also lives in a close symbiotic association with us. This human-associated microbiota, or human microbiome, is responsible for many key functions in our bodies. Increasing evidence suggests many important roles of individual members of the human microbiome and their respective influences towards ultimate health and disease of the host. This chapter highlights some of the important functions of the human microbiome, many of which were gleaned using different molecular approaches. The clinical field has thus greatly benefited from the molecular toolbox that was initially developed by microbial ecologists for investigation of other complex ecosystems, such as soil. As the field has progressively moved away from a dependence on cultivation-based approaches towards increasing reliance on molecular approaches, the amount of knowledge about the human microbiome composition and function has greatly expanded. Most recent studies using molecular tools, including various 'omics' approaches, have focused on the intestinal microbiota. Therefore, we have also primarily discussed the gut microbiota in this chapter. In addition, the influence of difference host-related factors, such as genetics, age, birth mode, diet and geographical location are discussed with respect to their impact on the composition and related function of the human microbiome. Some beneficial bacteria, such as probiotic strains, are discussed, in addition to those that are particularly detrimental to human health. Some of the latter include correlations of microbial compositions to intestinal diseases and cancer. The more information that we have about the key roles of specific members of the human microbiome, the more potential we have for manipulation of the composition of the microbiota to enhance the prevalence of beneficial species and to diminish the amounts of detrimental ones. This is a guiding vision for future research in this area.
10. Wastewater Treatment
Satoshi Okabe and Yoichi Kamagata
Of Earth's diverse microbial habitats, wastewater treatment processes are one of the most elaborate anthropogenic niches geared towards one purpose: cleaning up water. Recent application of molecular techniques is unveiling the microbial composition and architecture of the complex communities involved in the treatment processes. It is now recognized that wastewater processes harbor a vast variety of microorganisms most of which are yet-to-be cultured, hence uncharacterized. In this chapter, the latest knowledge on diversity, structure and functions of microbial communities in nitrifying processes, anaerobic ammonia oxidation processes and methane fermenting processes are summarized.
11. The Impact and Molecular Genetics of Bacterial Biofilms
Shuwen An, Yi-Hu Dong, Calvin Boon and Lian-Hui Zhang
Many bacteria can grow and live as biofilms, in which single microbial cells individually interconnect with each other through an extracellular matrix. Biofilm-forming bacteria pose severe problems in the environment, industry and health care sector due to increased bacterial survival competence in the environment and the protective nature of biofilms that prevent effective eradication. Technological progress in microscopy, molecular genetics and genome analysis has significantly advanced our understanding of the structural and molecular aspects of biofilms, especially of extensively studied model organisms such as Pseudomonas aeruginosa. Biofilm development can be divided into several key steps including attachment, microcolony formation, biofilm maturation and dispersion; and in each step bacteria may recruit different components and molecules including flagella, type IV pili, DNA and exopolysaccharides. The rapid progress in biofilm research has also unveiled several genetic regulation mechanisms implicated in biofilm regulation such as quorum sensing and the novel secondary messenger cyclic-di-GMP. Understanding the molecular mechanisms of biofilm formation has facilitated the exploration of novel strategies to control bacterial biofilms.
How to buy this book
(EAN: 9781904455523 9781912530915 Subjects: [bacteriology] [microbiology] [molecular microbiology] [genomics] [environmental microbiology] )